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This page was generated on 2023-02-27 02:34:30 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the CellaRepertorium package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellaRepertorium.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 268/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellaRepertorium 1.9.0 (landing page) Andrew McDavid
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: CellaRepertorium |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CellaRepertorium_1.9.0.tar.gz |
| StartedAt: 2023-02-24 08:30:18 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 08:35:44 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 325.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CellaRepertorium.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CellaRepertorium_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CellaRepertorium.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CellaRepertorium/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellaRepertorium’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellaRepertorium’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cross_tab_tbl: no visible binding for global variable ‘.’
cross_tab_tbl: no visible binding for global variable ‘x_key__’
fancy_name_contigs: no visible binding for global variable ‘.’
pairing_tables: no visible binding for global variable ‘.’
plot_cluster_factors: no visible binding for global variable ‘chain’
Undefined global functions or variables:
. chain x_key__
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/CellaRepertorium/libs/CellaRepertorium.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_cluster_factors 5.438 0.045 5.517
cluster_logistic_test 5.318 0.148 5.509
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘cdr3_clustering.Rmd’ using ‘UTF-8’... OK
‘cr-overview.Rmd’ using ‘UTF-8’... OK
‘mouse_tcell_qc.Rmd’ using ‘UTF-8’... OK
‘repertoire_and_expression.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/CellaRepertorium.Rcheck/00check.log’
for details.
CellaRepertorium.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CellaRepertorium
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘CellaRepertorium’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
160 | #pragma omp critical
|
cdhit-common.cpp:174: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
174 | #pragma omp critical
|
cdhit-common.cpp:2418: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2418 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:2435: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2435 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:2437: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas]
2437 | #pragma omp flush (stop)
|
cdhit-common.cpp:2458: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
2458 | #pragma omp critical
|
cdhit-common.cpp:2467: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas]
2467 | #pragma omp flush (stop)
|
cdhit-common.cpp:2492: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2492 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:3151: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
3151 | #pragma omp parallel for schedule( dynamic, 1 )
|
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In function ‘int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)’:
cdhit-common.cpp:545:13: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
545 | int max_diag = 0;
| ^~~~~~~~
cdhit-common.cpp: In function ‘int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)’:
cdhit-common.cpp:669:13: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
669 | int max_diag = 0;
| ^~~~~~~~
cdhit-common.cpp: In member function ‘void SequenceDB::SortDivide(Options&, bool)’:
cdhit-common.cpp:1774:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1774 | if (len > max_len) max_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp:1775:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1775 | if (len < min_len) min_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(int, const Options&)’:
cdhit-common.cpp:2379:16: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable]
2379 | size_t mem, mega = 1000000;
| ^~~
In file included from cdhit-common.cpp:37:
In member function ‘void NVector<TYPE>::Resize(int, const TYPE&) [with TYPE = long int]’,
inlined from ‘NVector<TYPE>::NVector(int, const TYPE&) [with TYPE = long int]’ at cdhit-common.h:124:10,
inlined from ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’ at cdhit-common.cpp:802:36:
cdhit-common.h:149:55: warning: argument 1 range [18446744056529682448, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
149 | items = (TYPE*)realloc( items, capacity*sizeof(TYPE) );
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdhit-common.h: In function ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’:
cdhit-common.h:149:55: note: in a call to built-in allocation function ‘void* __builtin_malloc(long unsigned int)’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c progress.cpp -o progress.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o CellaRepertorium.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CellaRepertorium)
CellaRepertorium.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CellaRepertorium)
>
> test_check("CellaRepertorium")
[ FAIL 0 | WARN 17 | SKIP 0 | PASS 81 ]
[ FAIL 0 | WARN 17 | SKIP 0 | PASS 81 ]
>
> proc.time()
user system elapsed
29.427 0.945 30.391
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
| name | user | system | elapsed | |
| ContigCellDB-fun | 0.246 | 0.000 | 0.250 | |
| canonicalize_cell | 0.450 | 0.000 | 0.453 | |
| canonicalize_cluster | 4.169 | 0.060 | 4.230 | |
| cash-ContigCellDB-method | 0.192 | 0.012 | 0.204 | |
| ccdb_join | 0.056 | 0.004 | 0.060 | |
| cdhit | 0.311 | 0.132 | 0.444 | |
| cdhit_ccdb | 0.184 | 0.012 | 0.196 | |
| cland | 4.031 | 0.044 | 4.077 | |
| cluster_filterset | 0.001 | 0.000 | 0.000 | |
| cluster_germline | 0.096 | 0.000 | 0.095 | |
| cluster_logistic_test | 5.318 | 0.148 | 5.509 | |
| cluster_permute_test | 1.067 | 0.056 | 1.131 | |
| cluster_plot | 3.031 | 0.032 | 3.063 | |
| cross_tab_tbl | 0.141 | 0.000 | 0.143 | |
| crosstab_by_celltype | 0.159 | 0.000 | 0.159 | |
| entropy | 0.004 | 0.000 | 0.004 | |
| enumerate_pairing | 0.817 | 0.000 | 0.817 | |
| equalize_ccdb | 0.084 | 0.000 | 0.084 | |
| fancy_name_contigs | 0.388 | 0.025 | 0.411 | |
| fine_cluster_seqs | 0.036 | 0.003 | 0.038 | |
| fine_clustering | 2.352 | 0.040 | 2.393 | |
| generate_pseudobulk | 0.180 | 0.008 | 0.188 | |
| guess_celltype | 0.069 | 0.008 | 0.076 | |
| hushWarning | 0.001 | 0.000 | 0.001 | |
| left_join_warn | 0.009 | 0.011 | 0.021 | |
| map_axis_labels | 0.242 | 0.008 | 0.254 | |
| mutate_cdb | 0.160 | 0.002 | 0.163 | |
| pairing_tables | 0.715 | 0.016 | 0.731 | |
| plot_cluster_factors | 5.438 | 0.045 | 5.517 | |
| purity | 0.001 | 0.000 | 0.000 | |
| rank_prevalence_ccdb | 0.440 | 0.004 | 0.444 | |
| rbind-ContigCellDB-method | 0.164 | 0.000 | 0.164 | |
| split_cdb | 0.076 | 0.000 | 0.077 | |
| sub-sub-ContigCellDB-character-missing-method | 0.048 | 0.015 | 0.063 | |